CyAbrB2 is a nucleoid-associated protein in <i>Synechocystis</i> controlling hydrogenase expression during fermentation.

Abstract

The <i>hox</i> operon in <i>Synechocystis</i> sp. PCC 6803, encoding bidirectional hydrogenase responsible for H₂ production, is transcriptionally upregulated under microoxic conditions. Although several regulators for <i>hox</i> transcription have been identified, their dynamics and higher-order DNA structure of <i>hox</i> region in microoxic conditions remain elusive. We focused on key regulators for the <i>hox</i> operon: cyAbrB2, a conserved regulator in cyanobacteria, and SigE, an alternative sigma factor. Chromatin immunoprecipitation sequencing revealed that cyAbrB2 binds to the <i>hox</i> promoter region under aerobic conditions, with its binding being flattened in microoxic conditions. Concurrently, SigE exhibited increased localization to the <i>hox</i> promoter under microoxic conditions. Genome-wide analysis revealed that cyAbrB2 binds broadly to AT-rich genome regions and represses gene expression. Moreover, we demonstrated the physical interactions of the <i>hox</i> promoter region with its distal genomic loci. Both the transition to microoxic conditions and the absence of cyAbrB2 influenced the chromosomal interaction. From these results, we propose that cyAbrB2 is a cyanobacterial nucleoid-associated protein (NAP), modulating chromosomal conformation, which blocks RNA polymerase from the <i>hox</i> promoter in aerobic conditions. We further infer that cyAbrB2, with altered localization pattern upon microoxic conditions, modifies chromosomal conformation in microoxic conditions, which allows SigE-containing RNA polymerase to access the <i>hox</i> promoter. The coordinated actions of this NAP and the alternative sigma factor are crucial for the proper <i>hox</i> expression in microoxic conditions. Our results highlight the impact of cyanobacterial chromosome conformation and NAPs on transcription, which have been insufficiently investigated.